chrX-125660469-A-G

Position:

• chrX-125660469-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.308 in 109,984 control chromosomes in the GnomAD database, including 3,948 homozygotes. There are 9,603 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (3948 hom., 9603 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.308 AC: 33903 AN: 109934 Hom.: 3949 Cov.: 22 AF XY: 0.297 AC XY: 9579 AN XY: 32218

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.308 AC: 33924 AN: 109984 Hom.: 3948 Cov.: 22 AF XY: 0.298 AC XY: 9603 AN XY: 32278

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.320

Alfa AF: 0.315 Hom.: 2356

Bravo AF: 0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10521734; hg19: chrX-124794465;